Contacts of the helix formed by residues 160 - 182 (chain A) in PDB entry 2B5F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 4.6 4.6 - - - +
159A TYR* 1.3 78.9 - - - +
161A LYS* 1.3 64.3 + - - +
162A GLY* 3.1 6.2 + - - +
163A THR* 2.9 32.1 + - - -
164A ALA* 3.1 22.0 + - - +
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 4.5 13.3 - - + +
160A ASN* 1.3 75.7 - - - +
162A GLY* 1.3 57.0 + - - +
164A ALA* 3.7 7.8 - - - +
165A LEU* 2.9 29.5 + - - +
240A ASP* 5.6 2.7 - - - -
241A ASP* 3.3 27.1 + - - +
243A TRP* 4.6 22.3 - - + +
244A ILE* 4.3 19.2 - - + +
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Residues in contact with GLY 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASN* 3.1 7.1 + - - -
161A LYS* 1.3 76.4 - - - +
163A THR* 1.3 58.4 + - - +
165A LEU* 3.5 7.9 + - - +
166A GLY* 3.0 23.7 + - - -
140B PHE* 4.0 3.6 - - - -
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Residues in contact with THR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 4.1 5.4 - - + -
160A ASN* 2.9 29.7 + - - -
162A GLY* 1.3 73.9 - - - +
164A ALA* 1.3 59.1 + - - +
166A GLY 3.2 0.7 + - - -
167A ALA* 2.9 30.0 + - + +
216A ILE* 3.6 25.8 - - + -
139B ALA 4.7 1.4 + - - -
140B PHE* 3.1 56.3 + - + +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.9 15.5 - - + -
159A TYR* 5.4 1.5 - - + +
160A ASN 3.1 10.8 + - - +
161A LYS 3.7 7.2 - - - +
163A THR* 1.3 78.8 - - - +
165A LEU* 1.3 63.9 + - - +
167A ALA* 3.2 2.3 + - - +
168A GLU* 2.9 28.4 + - - +
216A ILE* 4.1 7.2 - - + -
217A THR* 3.3 31.6 + - + -
244A ILE* 4.2 9.9 - - + -
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LYS 2.9 18.7 + - - +
162A GLY* 3.9 7.4 - - - +
164A ALA* 1.3 77.9 - - - +
166A GLY* 1.3 62.0 + - - +
168A GLU* 3.2 3.2 + - - +
169A ILE* 2.9 40.2 + - + +
243A TRP* 4.2 26.0 - - + -
244A ILE* 3.9 19.2 - - + +
247A VAL* 4.3 13.5 - - + -
248A GLY* 3.5 35.7 - - - +
251A ILE* 5.5 2.7 - - + -
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A GLY 3.0 12.0 + - - -
163A THR 3.2 0.6 + - - -
165A LEU* 1.3 76.6 - - - +
167A ALA* 1.3 55.4 + - - +
169A ILE* 3.3 13.3 + - - +
170A ILE* 3.0 30.0 + - - +
140B PHE* 3.3 31.0 - - - -
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A THR 2.9 16.9 + - - +
164A ALA 3.7 4.0 - - - +
166A GLY* 1.3 76.1 - - - +
168A GLU* 1.3 58.0 + - + +
170A ILE* 3.9 2.1 - - - +
171A GLY* 2.9 28.1 + - - -
213A THR* 4.5 16.5 + - + +
216A ILE* 3.8 27.1 - - + -
221A ILE* 5.3 0.2 - - - +
53B TYR* 3.7 22.2 + - - +
140B PHE* 4.0 4.6 - - + -
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA 2.9 19.5 + - - +
165A LEU* 3.7 5.2 - - - +
167A ALA* 1.3 75.6 - - - +
169A ILE* 1.3 58.0 + - - +
172A THR* 2.7 37.2 + - - -
213A THR* 4.1 3.3 - - - +
217A THR* 2.8 21.5 + - - +
219A THR* 3.4 4.7 - - - -
220A GLY* 3.0 21.2 + - - -
221A ILE* 2.7 34.1 + - - +
244A ILE* 4.3 8.5 - - + +
245A PHE* 3.5 25.4 - - + -
248A GLY* 4.1 16.7 - - - +
249A PRO* 4.1 5.6 - - + +
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Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 2.9 37.6 + - + +
166A GLY* 3.3 11.4 + - - +
168A GLU* 1.3 76.8 - - - +
170A ILE* 1.3 61.4 + - + +
172A THR 3.4 0.5 + - - -
173A PHE* 2.9 26.9 + - + +
248A GLY* 3.6 25.6 - - - +
251A ILE* 4.0 29.6 - - + -
252A GLY* 3.3 18.9 - - - -
255A VAL* 5.2 6.5 - - + -
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Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY 3.0 11.3 + - - +
167A ALA 3.9 2.9 - - - +
169A ILE* 1.3 80.3 - - + +
171A GLY* 1.3 69.7 + - - +
173A PHE* 3.2 9.9 + - + +
174A VAL* 3.0 28.2 + - + +
49B LEU* 4.7 4.3 - - + -
50B LEU* 3.1 35.4 - - + -
53B TYR* 3.3 56.8 - - + +
140B PHE* 6.3 1.6 - - + -
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Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA 2.9 19.3 + - - -
168A GLU 4.0 0.4 - - - -
170A ILE* 1.3 78.9 - - - +
172A THR* 1.3 60.0 + - - +
174A VAL* 3.4 2.7 + - - -
175A LEU* 3.3 18.7 + - - +
209A VAL* 3.6 36.0 - - - +
213A THR* 5.1 1.1 - - - -
221A ILE* 3.9 8.4 - - - +
53B TYR* 5.6 0.9 - - - -
54B ILE* 5.7 0.9 - - - -
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA* 4.0 13.0 - - + -
168A GLU 2.7 21.8 + - - -
169A ILE 3.8 2.7 - - - -
171A GLY* 1.3 73.0 - - - +
173A PHE* 1.3 61.1 + - - +
175A LEU* 3.2 5.9 + - + +
176A VAL* 2.9 38.3 + - + +
221A ILE* 3.4 27.7 - - - +
249A PRO* 3.3 45.1 - - + +
252A GLY* 4.3 2.2 - - - -
253A ALA 4.1 0.9 - - - +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 2.9 16.5 + - + +
170A ILE* 3.3 14.4 - - + +
172A THR* 1.3 72.7 - - - +
174A VAL* 1.3 65.1 + - - +
177A TYR* 2.8 45.1 + + + +
252A GLY* 3.7 11.3 + - - +
255A VAL* 3.7 23.8 - - + -
256A ALA* 3.4 38.8 - - + -
259A TYR* 4.0 28.3 - + + -
46B ILE* 4.5 10.5 - - + -
50B LEU* 3.4 34.1 - - + -
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ILE* 3.0 20.5 + - + +
171A GLY 3.6 8.1 - - - +
172A THR 3.3 0.2 - - - -
173A PHE* 1.3 75.9 - - - +
175A LEU* 1.3 57.4 + - - +
177A TYR* 3.7 4.6 - - + +
178A THR* 2.6 38.9 + - - +
205A ALA* 4.3 10.1 - - + +
208A MET* 5.7 0.2 - - + -
209A VAL* 3.8 17.0 - - + -
50B LEU* 3.5 34.8 - - + -
54B ILE* 4.2 16.8 - - + -
84B MET* 4.5 20.0 - - + -
87B VAL* 5.1 4.9 - - + -
88B LEU* 6.3 0.9 - - + -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASN* 3.5 28.5 - - - +
103A ALA* 6.0 0.2 - - + -
104A VAL* 4.2 10.8 - - + -
171A GLY 3.3 8.9 + - - +
172A THR* 3.2 9.4 + - + +
173A PHE 3.2 0.8 - - - -
174A VAL* 1.3 79.9 - - - +
176A VAL* 1.3 65.2 + - + +
178A THR* 3.1 7.1 + - - -
179A VAL* 2.9 31.8 + - + +
202A ILE* 3.7 31.2 - - + -
205A ALA* 4.5 10.5 + - + +
206A VAL* 3.8 11.9 - - + -
221A ILE* 3.7 27.6 - - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ALA 4.2 12.8 - - - +
104A VAL* 4.5 10.1 - - + +
107A GLY* 4.7 5.6 - - - -
108A LEU* 5.8 0.4 - - + +
172A THR* 2.9 30.3 + - + +
175A LEU* 1.3 77.1 - - + +
177A TYR* 1.3 64.4 + - - +
179A VAL* 3.2 9.0 + - + +
180A PHE* 3.0 43.4 + - + -
253A ALA* 4.0 29.6 - - + +
256A ALA* 3.8 20.2 - - + -
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 2.8 41.1 + + + +
174A VAL* 3.7 4.7 - - + +
176A VAL* 1.3 77.3 - - - +
178A THR* 1.3 60.3 + - - +
180A PHE* 3.5 4.0 + - - +
181A SER* 2.9 41.0 + - - -
256A ALA* 3.8 10.1 - - + +
259A TYR* 4.0 34.6 + + + -
260A HIS* 4.7 13.9 - + - -
263A VAL* 5.6 5.8 - - + +
43B ALA* 5.2 4.0 + - - +
46B ILE* 4.8 9.1 - - + +
47B ALA* 5.9 1.8 - - - -
50B LEU* 4.8 7.9 - - + -
87B VAL* 6.5 0.2 - - + -
88B LEU* 4.9 14.1 - - + -
91B CYS* 3.6 35.6 + - + +
92B THR* 3.7 16.7 - - + +
95B ILE* 6.0 0.5 - - - +
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A VAL* 2.6 22.1 + - - +
175A LEU 3.1 7.4 + - - -
177A TYR* 1.3 77.7 - - - +
179A VAL* 1.3 52.0 + - - +
181A SER* 3.1 4.3 + - - -
182A ALA* 2.7 35.2 + - + +
201A PRO* 3.8 27.8 - - + +
202A ILE* 4.4 4.7 - - + +
205A ALA* 3.4 27.5 - - + +
87B VAL* 3.6 21.9 - - + +
90B TYR* 4.8 3.0 - - + -
91B CYS* 4.0 14.1 - - - -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 4.2 33.4 - - + -
108A LEU* 4.5 21.8 - - + -
175A LEU* 2.9 28.5 + - + +
176A VAL* 3.2 12.1 + - + +
178A THR* 1.3 74.7 - - - +
180A PHE* 1.3 58.1 + - + +
182A ALA* 2.5 34.7 + - + +
183A THR* 3.1 11.4 + - - +
202A ILE* 3.7 24.5 - - + -
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLY 3.4 27.4 - - - -
108A LEU* 3.9 23.6 - - + -
111A ALA* 4.0 17.7 - - + -
176A VAL* 3.0 42.5 + - + +
177A TYR* 3.9 2.5 - - - +
179A VAL* 1.3 72.7 - - + +
181A SER* 1.3 66.5 + - - +
182A ALA 3.2 0.5 + - - -
183A THR* 3.3 24.9 + - + +
256A ALA 4.5 2.9 - - - -
257A ALA* 3.5 31.0 - - + -
260A HIS* 3.1 45.5 + + + -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A TYR* 2.9 25.2 + - - -
178A THR 3.1 7.2 + - - -
180A PHE* 1.3 80.9 - - - +
182A ALA* 1.3 56.7 + - - +
183A THR 3.1 9.4 + - - +
184A ASP* 4.6 1.7 - - - +
260A HIS* 4.1 9.9 + - - -
90B TYR* 3.3 21.7 + - - -
91B CYS* 3.8 33.3 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A THR* 2.7 15.7 + - + +
179A VAL* 2.5 30.6 + - + +
181A SER* 1.3 71.8 - - - +
183A THR* 1.3 55.4 + - - +
184A ASP* 4.2 9.2 - - - +
198A ALA* 4.3 30.3 - - - +
201A PRO* 5.1 2.2 - - + -
202A ILE* 4.6 10.8 - - + -
90B TYR* 3.8 15.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il